a Microsatellites whose repeat unit is not composed exclusively of the nucleotides A and T, b Total numberof microsatellites occurring in a region where the alignment depth is greater than one, c Total numberof microsatellites for which we observed more than one allele in our EST collection.
Finally, we use this knowledge to develop a test statistic sensitive to microsatellite selection, which we then apply in an illustrative scan for microsatellite selection in the CEPH population sampled from Utah (CEU).
Further, these microsatellite loci, which we used because they had been previously studied in a worldwide collection of individuals, might not be representative of all human microsatellites.
Using SSR-1, -2, and -3 microsatellites, which all contain (CAG), we found no Y chromosome-specific markers.
From these, we selected 24 microsatellites, which showed at least 10 repeats (13 dinucleotides and 11 trinucleotides) for further analyses.
To this end, we identified 5,128 non-redundant microsatellites, which were subsequently analyzed elsewhere for polymorphisms (see methods).
Using this tool, we examined the association between highly conserved microsatellites and gene promoters, which we defined as 2,000 bp upstream and downstream of the canonical transcription start site.
In addition we compare sequence variation between the two fox species and the dog (Canis lupus), and we provide a resource of potential variable microsatellites, which will be useful in future population studies.
After removing unsuitable loci and including potentially heterozygous loci, a total of 1277 microsatellite regions remained, for which we attempted to design primers using Primer3 within Geneious (Rozen and Skaletsky, 2000).
